Showing : affycoretools • reset
0
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*** caught segfault *** , cause 'memory not mapped'
affycoretools FRMA affyio AffymetrixDataTestFiles affy
updated 5 months ago by 63k • written 6 months ago by • 0
1
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1
reply
579
views
affycoretools - improve error message in annotateEset(ExpressionSet, AffyExpressionPDInfo)
affycoretools
updated 22 months ago by 63k • written 22 months ago by ▴ 180
1
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1
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726
views
affycoretools - include percent variance explained in plotPCA()
affycoretools
updated 22 months ago by 63k • written 22 months ago by ▴ 180
1
vote
1
reply
587
views
afffycoretools - warnings in mirna2mrna()
affycoretools DBI
updated 22 months ago by 63k • written 22 months ago by ▴ 180
0
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3
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1.1k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 2.8 years ago by 63k • written 2.8 years ago by • 0
0
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2
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1.0k
views
oligo package - aggregate transcript expression to gene
affycoretools oligo
2.9 years ago Luca • 0
5
votes
5
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910
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Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 3.5 years ago by 63k • written 3.5 years ago by ▴ 810
3
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5
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1.0k
views
affycoretools::annotateEset(eset, pd.ht.hgu133.plus.pm) return error
affycoretools annotation HT HG-U133+ PM Array
updated 3.8 years ago by 63k • written 3.8 years ago by ▴ 40
1
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2
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1.1k
views
Inconsistent results when normalizing HTA2.0 arrays at "level=core"
oligo HTA2.0 affycoretools RMA fitProbeLevelModel
updated 4.2 years ago by 63k • written 4.2 years ago by ★ 3.7k
1
vote
5
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868
views
Correct annotation R package for human clariom array analysis
clariom oligo affycoretools pd.hugene.2.0.st
updated 4.5 years ago by 63k • written 4.5 years ago by ▴ 810
0
votes
3
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1.5k
views
affycoretools::annotateEset unable to find inherited method
affycoretools missing file link annotateEset
updated 5.3 years ago by 63k • written 5.3 years ago by • 0
2
votes
4
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1.0k
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 5.6 years ago by 63k • written 5.6 years ago by ▴ 10
1
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3
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1.0k
views
Different microarrays annotations provided by toTable and annotateEset functions
microarray annotation annotationdbi affycoretools annotationtools
updated 5.7 years ago by 63k • written 5.7 years ago by ▴ 70
2
votes
4
replies
1.9k
views
affycoretools annotateEset problem using Clariom D arrays
affycoretools clariom
updated 6.1 years ago by 63k • written 6.1 years ago by ▴ 30
2
votes
3
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1.3k
views
Filtering of lowly expressed probes in HTA 2.0 using new pd.hta.2.0 version 3.12.2
pd.hta.2.0 hta2.0 affycoretools
updated 6.1 years ago by 63k • written 6.1 years ago by ▴ 20
6
votes
7
replies
2.9k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo affycoretools hta2.0 affymetrix
updated 16 months ago by ▴ 10 • written 6.5 years ago by ▴ 810
9
votes
6
replies
3.6k
views
Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options
microarray oligo affycoretools pd.hugene.2.0.st hugene20sttranscriptcluster.db
updated 6.6 years ago by 63k • written 6.6 years ago by ▴ 810
0
votes
3
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1.2k
views
Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."
affycoretools
updated 6.7 years ago by 63k • written 6.7 years ago by ★ 2.0k
3
votes
5
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1.2k
views
affycoretools' plotPCA no longer can do 3D plot?
affycoretools
updated 8.4 years ago by 63k • written 8.4 years ago by ★ 2.0k
0
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4
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2.7k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 9.4 years ago by 40k • written 9.4 years ago by ▴ 50
0
votes
3
replies
1.8k
views
trouble installing affycoretools for R 3.0
VariantAnnotation GO BSgenome affycoretools BSgenome VariantAnnotation ggbio GO BSgenome
updated 10.5 years ago by 63k • written 10.5 years ago by ★ 2.0k
0
votes
0
replies
1.2k
views
identifying drosophila miRNA targets
miRNA drosophila2 probe affy convert affycoretools microRNA miRNA drosophila2 probe affy
10.5 years ago Fiona ▴ 70
0
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7
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1.3k
views
vennSelect error
GO hgu133a2 yeast2 affy affycoretools GO hgu133a2 yeast2 affy affycoretools
updated 12.3 years ago by 63k • written 12.3 years ago by ▴ 370
0
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1
reply
950
views
why kOverA function has 6
affycoretools affycoretools
updated 12.4 years ago by ▴ 20 • written 12.4 years ago by ★ 2.0k
0
votes
0
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970
views
quality control of affy Chips for miRNA
miRNA cdf probe affy simpleaffy affyQCReport affycoretools arrayQualityMetrics miRNA cdf
12.6 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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902
views
quality control of affy Chips for miRNA
miRNA cdf affy simpleaffy affyQCReport affycoretools miRNA cdf affy simpleaffy
updated 12.6 years ago by 63k • written 12.6 years ago by ★ 1.5k
0
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3
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1.4k
views
Help in installing affycoretools
affycoretools affycoretools
updated 13.9 years ago by 25k • written 13.9 years ago by ▴ 350
0
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0
replies
968
views
Annotation.db: how automatically call a mapping?
Annotation GO moe430a affy limma annaffy affycoretools Annotation GO moe430a affy limma
14.2 years ago James W. MacDonald 63k
0
votes
4
replies
3.9k
views
Extracting genes within venn diagram
limma affycoretools limma affycoretools
14.9 years ago Celine Carret ▴ 220
0
votes
0
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915
views
problem installing affycoretools in R in linux environment
GO biomaRt affycoretools GO biomaRt affycoretools
15.0 years ago James W. MacDonald 63k
0
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2
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1.5k
views
problem installing affycoretools in R in linux environment
GO affycoretools GO affycoretools
updated 15.0 years ago by 63k • written 15.0 years ago by ▴ 80
0
votes
0
replies
911
views
problem installing affycoretools in R in linux environment
GO Cancer biomaRt affycoretools GO Cancer biomaRt affycoretools
15.0 years ago rgentleman ★ 5.5k
0
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3
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1.2k
views
affycoretools repost
GO limma affycoretools GO limma affycoretools
updated 15.3 years ago by 63k • written 15.3 years ago by ▴ 160
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1
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1.1k
views
affycoretools question
GO limma affycoretools GO limma affycoretools
updated 15.3 years ago by 63k • written 15.3 years ago by ▴ 160
0
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10
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1.4k
views
Problem with invalid GO term in HyperGResult object - NOT solved
GO Cancer GOstats affycoretools GO Cancer GOstats affycoretools
updated 16.0 years ago by ★ 2.2k • written 16.0 years ago by ★ 7.4k
0
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3
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1.0k
views
intended behavior of plotPCA and AffyBatch objects?
affy affycoretools affy affycoretools
updated 16.4 years ago by 63k • written 16.4 years ago by ★ 2.2k
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3
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1.6k
views
Can't get RCurl...
GO Survival annotate genefilter affy graph limma GOstats biomaRt Category affycoretools
updated 16.5 years ago by 63k • written 16.5 years ago by ★ 2.2k
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2
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1.4k
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
GO Survival Biobase genefilter affy limma RBGL GOstats Category affyio affycoretools GO
16.6 years ago Mark W Kimpel ▴ 830
0
votes
1
reply
667
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
affycoretools affycoretools
updated 16.6 years ago by 63k • written 16.6 years ago by ▴ 830
0
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5
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1.3k
views
error coercing an exprSet to ExpressionSet
GO cdf Biobase annotate multtest affy limma RBGL GOstats Category affycoretools GO cdf
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 890
0
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0
replies
891
views
help with RankProd plaase
GO Survival cdf genefilter multtest affy limma RankProd Category affycoretools GO cdf
16.9 years ago Kimpel, Mark W ▴ 890
0
votes
3
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3.6k
views
PCA-prcomp() versus plotPCA
affycoretools affycoretools
updated 16.9 years ago by 63k • written 16.9 years ago by ▴ 320
0
votes
0
replies
979
views
question_gene list from venn diagram limma function for two color array data
Microarray Annotation Cancer GOstats affycoretools Microarray Annotation Cancer GOstats
16.9 years ago James W. MacDonald 63k
0
votes
2
replies
1.1k
views
problem with latest version of graph
GO annotate genefilter multtest affy graph Rgraphviz RBGL GOstats affyio affycoretools
17.3 years ago Kimpel, Mark W ▴ 890
0
votes
1
reply
793
views
affycoretools limma2annaffy fold change output question
affycoretools affycoretools
updated 17.5 years ago by 63k • written 17.5 years ago by ▴ 890
0
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6
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1.3k
views
RNA degradation tends & options for analysis
affy limma gcrma affycoretools affy limma gcrma affycoretools
updated 17.6 years ago by 63k • written 17.6 years ago by ▴ 20
0
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2
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904
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justRMA using incorrect default cdf
GO Survival rat2302 cdf annotate genefilter affy limma affycoretools GO Survival cdf
17.6 years ago Kimpel, Mark W ▴ 890
47 results • Page 1 of 1
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Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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